BOSTON — Boston University won final federal approval Thursday for a controversial plan to build a research laboratory in the city’s South End that would handle some of the world’s most dangerous and exotic germs.

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The decision by the National Institutes of Health secures $128 million in federal funding for the lab, which will be part of a national group of facilities that will study infectious diseases such as ebola and the West Nile virus.

University officials said the lab will be safe and will provide needed research into contagious illnesses and the risk they might pose in the hands of bioterrorists.

But opponents have criticized the decision to build the lab in a densely populated urban neighborhood.

The controversy escalated in 2004, when three workers at another BU lab became sick after they were exposed to a highly infectious strain of tularemia, or rabbit fever. They recovered.

Construction is scheduled to begin this month and should be complete by 2008. The university estimates the new lab will create more than 650 permanent jobs and contribute nearly $3 billion to the local economy over the next 20 years.

“We are proud to be part of the national network of dedicated scientists and researchers who will use this state-of-the-art facility to safely find treatments and cures for some of the most dangerous infectious diseases that threaten Boston, the nation and the world,” said Dr. Mark Klempner, lead investigator for the new lab.